Justyna Kalinowska-Tłuścik

Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment

Background2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery.ResultsEfficient recombinant protein production and crystallization protocols were developed, and high-resolution crystal structures of IspF from P. falciparum (Pf IspF) and B. cenocepacia (Bc IspF) in complex with cytidine nucleotides determined. Comparisons with orthologues, indicate a high degree of order and conservation in parts of the active site where Zn2+ is bound and where recognition of the cytidine moiety of substrate occurs. However, conformational flexibility is noted in that area of the active site responsible for binding the methylerythritol component of substrate. Unexpectedly, one structure of Bc IspF revealed two molecules of cytidine monophosphate in the active site, and another identified citrate coordinating to the catalytic Zn2+. In both cases interactions with ligands appear to help order a flexible loop at one side of the active site. Difficulties were encountered when attempting to derive complex structures with other ligands.ConclusionsHigh-resolution crystal structures of IspF from two important human pathogens have been obtained and compared to orthologues. The studies reveal new data on ligand binding, with citrate coordinating to the active site Zn2+ and when present in high concentrations cytidine monophosphate displays two binding modes in the active site. Ligand binding appears to order a part of the active site involved in substrate recognition. The high degree of structural conservation in and around the IspF active site suggests that any structural model might be suitable to support a program of structure-based drug discovery.

Versatile Multicomponent Reaction Macrocycle Synthesis Using α-Isocyano-ω-carboxylic Acids

The direct macrocycle synthesis of α-isocyano-ω-carboxylic acids via an Ugi multicomponent reaction is introduced. This multicomponent reaction (MCR) protocol differs by being especially short, convergent, and versatile, giving access to 12-22 membered rings.

α‐Amino Acid‐Isosteric α‐Amino Tetrazoles

The synthesis of all 20 common natural proteinogenic and 4 otherα-amino acid-isosteric α-amino tetrazoles has been accomplished, whereby the carboxyl group is replaced by the isosteric 5-tetrazolyl group. The short process involves the use of the key Ugi tetrazole reaction followed by deprotection chemistries. The tetrazole group is bioisosteric to the carboxylic acid and is widely used in medicinal chemistry and drug design. Surprisingly, several of the common α-amino acid-isosteric α-amino tetrazoles are unknown up to now. Therefore a rapid synthetic access to this compound class and non-natural derivatives is of high interest to advance the field.

De Novo Assembly of Highly Substituted Morpholines and Piperazines

The morpholine and piperazine with their remarkable physical and biochemical properties are popular heterocycles in organic and medicinal chemistry used in rational property design. However, in the majority of cases these rings are added to an existing molecule in a building block approach thus limiting their substitution pattern and diversity. Here we introduce a versatile de novo synthesis of the morpholine and piperazine rings using multicomponent reaction chemistry. The large scale amenable building blocks can be further substituted at up to four positions, making this a very versatile scaffold synthesis strategy. Our methods thus fulfill the increasing demand for novel building block design and nontraditional scaffolds which previously were not accessible

Two‐Step Synthesis of Complex Artificial Macrocyclic Compounds

The design and synthesis of head-to-tail linked artificial macrocycles using the Ugi-reaction has been developed. This synthetic approach of just two steps is unprecedented, short, efficient and works over a wide range of medium (8-11) and macrocyclic (≥12) loop sizes. The substrate scope and functional group tolerance is exceptional. Using this approach, we have synthesized 39 novel macrocycles by two or even one single synthetic operation. The properties of our macrocycles are discussed with respect to their potential to bind to biological targets that are not druggable by conventional, drug-like compounds. As an application of these artificial macrocycles we highlight potent p53-MDM2 antagonism.

Rational design of 5-HT6R ligands using a bioisosteric strategy: synthesis, biological evaluation and molecular modelling

A bioisosteric strategy was successfully implemented with a screening protocol for new, potent 5-HT6R ligands. Initially, 2-[5-(4-methylpiperazin-1-yl)-2-nitrophenyl]-1,2,3,4-tetrahydroisoquinoline (9) was found in commercial databases using a bioisosteric query (screening 5-HT6R Ki = 128 nM). Then, the hit compound was bioisosterically modified (ring alteration) leading to a novel, high affinity (Ki = 6 nM) 5-HT6R ligand (10). Extensive docking studies followed by structural interaction fingerprint analysis supported by single-crystal X-ray structures of the investigated ligands suggest different binding modes with 5-HT6R models for compounds with varying activity. An alternative anchoring point for protonated amine (D7.36) that has not been previously reported was identified.

Arylpiperazinylalkyl derivatives of 8-amino-1,3-dimethylpurine-2,6-dione as novel multitarget 5-HT/D receptor agents with potential antipsychotic activity.

Abstract A series of new 7-arylpiperazinylalkyl-1,3-dimethyl-purine-2,6-dione derivatives with diversified 8-amino substituent in 8 position was synthesized and their 5-HT1A, 5-HT2A, 5-HT6, 5-HT7, and D2 receptor affinities were determined. The binding study allowed identifying some potent 5-HT1A/5-HT2A/5-HT7/D2 ligands. The most interesting because of their multireceptor profile were 8-piperidine (30–35) and 8-dipropylamine (45–47) analogs with four and five carbon aliphatic linkers. The selected compounds 24, 31, 34, 39, 41, 43, 45, and 46 in the functional in vitro evaluation for all targeted receptors showed significant partial D2 agonist, partial 5-HT1A agonist, and 5-HT2A antagonist properties. The advantageous in vitro affinity of compound 34 for 5-HT1A and D2 receptors has been explained by means of molecular modeling, taking into consideration its partial agonist activity towards the latter one. In behavioral studies, compounds 32 and 34 revealed antipsychotic-like properties, significantly decreasing d-amphetamine-induced hyperactivity in mice.

Versatile Protecting-Group Free Tetrazolomethane Amine Synthesis by Ugi Reaction.

The use of ammonia in the Ugi reaction is often problematic due to low yields and multiple side reactions. Here, we report the use of ammonia in the tetrazole Ugi variation providing a clean, good-to-high yielding reaction, especially with ketones as oxo components. The scope and limitations of this reaction and a structure-reactivity relationship are provided by performing >85 reactions. The primary amine component of the α-amino tetrazole is a versatile starting material for further reactions.

Ratiometric fluorescent Zn2+ and In3+ receptors of fused pyrazine with an aminopropanol chain in acetonitrile

A series of new potential intramolecular charge transfer ICT fluorescent receptors of Zn2+, Cd2+, Hg2+, Ga3+, In3+, and Tl3+ ions based on N-aryl or N-alkyl variously fused pyridopyrrolopyrazine or pyrrolo[2,3-b]quinoxaline with an integrated donor group, such as 3-aminopropanol, were synthesized and verified. Among [N, N, O] tridentate donors 4a, 6a–d, 10a, 12e, and 14e, only the integrated fluorophore-receptors with the nitrogen atom at the N-5 position of heterocyclic systems, pyrido[2,3-b]pyrrolo[2,3-e]pyrazine 6a, selectively respond to zinc and indium with significant fluorescent enhancement and different mechanisms of binding. The first example of Z to E interconversion of enaminone forms of a ligand responsible for Zn2+ complex fluorescence enhancement was documented.

Concise Synthesis of Tetrazole Macrocycle

A concise two step synthesis of tetrazole containing macrocycles from readily accessible starting materials is presented. The first step comprises a chemoselective amidation of amino acid derived isocyanocarboxylicacid esters with unprotected symmetrical diamines to afford diverse α-isocyano-ω-amines. In the second step, the α-isocyano-ω-amines undergo an Ugi tetrazole reaction to close the macrocycle. Advantageously, this strategy allows short access to 11–19-membered macrocycles in which substituents can be independently varied at three different positions.